1
|
Somers T, Allard NAE, Siddiqi S, Janssen MCM, Hopman MTE, Morshuis WJ, Russel FGM, Timmers S, Schirris TJJ. Mitochondrial complex III activity: from invasive muscle biopsies to patient-friendly buccal swab analysis. Sci Rep 2023; 13:9638. [PMID: 37316639 DOI: 10.1038/s41598-023-36741-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023] Open
Abstract
Drug-induced mitochondrial dysfunction is a common adverse effect, particularly in case of statins-the most prescribed drugs worldwide. These drugs have been shown to inhibit complex III (CIII) of the mitochondrial oxidative phosphorylation process, which is related to muscle pain. As muscle pain is the most common complaint of statin users, it is crucial to distinguish it from other causes of myalgia to prevent unnecessary cessation of drug therapy. However, diagnosing CIII inhibition currently requires muscle biopsies, which are invasive and not practical for routine testing. Less invasive alternatives for measurement of mitochondrial complex activities are only available yet for complex I and IV. Here, we describe a non-invasive spectrophotometric method to determine CIII catalytic activities using buccal swabs, which we validated in a cohort of statin and non-statin users. Our data indicate that CIII can be reliably measured in buccal swabs, as evidenced by reproducible results above the detection limit. Further validation on a large-scale clinical setting is recommended.
Collapse
Affiliation(s)
- Tim Somers
- Department of Cardiothoracic Surgery, Radboud University Medical Center, Geert Grooteplein Zuid 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Department of Pharmacology and Toxicology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.
| | - Neeltje A E Allard
- Department of Physiology, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sailay Siddiqi
- Department of Cardiothoracic Surgery, Radboud University Medical Center, Geert Grooteplein Zuid 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Margit C M Janssen
- Department of Pharmacology and Toxicology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Maria T E Hopman
- Department of Physiology, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Wim J Morshuis
- Department of Cardiothoracic Surgery, Radboud University Medical Center, Geert Grooteplein Zuid 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Frans G M Russel
- Department of Pharmacology and Toxicology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Silvie Timmers
- Department of Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Tom J J Schirris
- Department of Pharmacology and Toxicology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| |
Collapse
|
2
|
Kumar A, Skrahina V, Atta J, Boettcher V, Hanig N, Rolfs A, Oprea G, Ameziane N. Microbial contamination and composition of oral samples subjected to clinical whole genome sequencing. Front Genet 2023; 14:1081424. [PMID: 36824435 PMCID: PMC9941560 DOI: 10.3389/fgene.2023.1081424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/24/2023] [Indexed: 02/10/2023] Open
Abstract
Biological material from the oral cavity is an excellent source of samples for genetic diagnostics. This is because collection is quick, easy-to-access, and non-invasive. We have set-up clinical whole genome sequence testing for patients with suspected hereditary disease. Beside the excellent quality of human DNA that can be isolated from such samples, we observed the presence of non-human DNA sequences at varying percentages. We investigated the proportion of non-human mapped reads (NHMR) sequenced from buccal swabs and saliva, the type of microbial genomes from which they were derived, and impact on molecular classification. Read sequences that did not map to the human reference genome were aligned to complete reference microbial reference sequences from the National Center for Biotechnology Information's (NCBI) RefSeq database using Kraken2. Out of 765 analyzed samples over 80% demonstrated more than 5% NHMRs. The majority of NHMRs were from bacterial genomes (average 69%, buccal swabs and 54% saliva), while the proportion of viruses was low, averaging 0.32% (buccal swabs) and 0.07% (saliva). We identified more than 30 different bacterial families of which Streptococcus mitis and Rothia mucilaginosa were the most common species. Importantly, the level of contamination did not impact the diagnostic yield.
Collapse
Affiliation(s)
| | | | | | | | | | - Arndt Rolfs
- Arcensus Diagnostics, Rostock, Germany,Medical Faculty University of Rostock, Rostock, Germany
| | | | - Najim Ameziane
- Arcensus Diagnostics, Rostock, Germany,*Correspondence: Najim Ameziane,
| |
Collapse
|
3
|
Acin-Perez R, Benincá C, Shabane B, Shirihai OS, Stiles L. Utilization of Human Samples for Assessment of Mitochondrial Bioenergetics: Gold Standards, Limitations, and Future Perspectives. Life (Basel) 2021; 11:949. [PMID: 34575097 PMCID: PMC8467772 DOI: 10.3390/life11090949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/12/2021] [Accepted: 08/23/2021] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial bioenergetic function is a central component of cellular metabolism in health and disease. Mitochondrial oxidative phosphorylation is critical for maintaining energetic homeostasis, and impairment of mitochondrial function underlies the development and progression of metabolic diseases and aging. However, measurement of mitochondrial bioenergetic function can be challenging in human samples due to limitations in the size of the collected sample. Furthermore, the collection of samples from human cohorts is often spread over multiple days and locations, which makes immediate sample processing and bioenergetics analysis challenging. Therefore, sample selection and choice of tests should be carefully considered. Basic research, clinical trials, and mitochondrial disease diagnosis rely primarily on skeletal muscle samples. However, obtaining skeletal muscle biopsies requires an appropriate clinical setting and specialized personnel, making skeletal muscle a less suitable tissue for certain research studies. Circulating white blood cells and platelets offer a promising primary tissue alternative to biopsies for the study of mitochondrial bioenergetics. Recent advances in frozen respirometry protocols combined with the utilization of minimally invasive and non-invasive samples may provide promise for future mitochondrial research studies in humans. Here we review the human samples commonly used for the measurement of mitochondrial bioenergetics with a focus on the advantages and limitations of each sample.
Collapse
Affiliation(s)
- Rebeca Acin-Perez
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; (C.B.); (B.S.); (O.S.S.)
- Metabolism Theme, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Cristiane Benincá
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; (C.B.); (B.S.); (O.S.S.)
- Metabolism Theme, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Byourak Shabane
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; (C.B.); (B.S.); (O.S.S.)
- Metabolism Theme, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Orian S. Shirihai
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; (C.B.); (B.S.); (O.S.S.)
- Metabolism Theme, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Linsey Stiles
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; (C.B.); (B.S.); (O.S.S.)
- Metabolism Theme, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
4
|
De Nys S, Duca RC, Nawrot T, Hoet P, Van Meerbeek B, Van Landuyt KL, Godderis L. Temporal variability of global DNA methylation and hydroxymethylation in buccal cells of healthy adults: Association with air pollution. ENVIRONMENT INTERNATIONAL 2018; 111:301-308. [PMID: 29217223 DOI: 10.1016/j.envint.2017.11.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/11/2017] [Accepted: 11/02/2017] [Indexed: 05/17/2023]
Abstract
BACKGROUND Epigenetic changes, such as DNA methylation, are observed in response to environmental exposure and in the development of several chronic diseases. Consequently, DNA methylation alterations might serve as indicators of early effects. In this context, the aim of this study was to assess the temporal variability of global DNA methylation and hydroxymethylation levels in buccal cells from healthy adult volunteers. METHODS Global DNA methylation (%5mdC) and hydroxymethylation (%5hmdC) levels in human buccal cells, collected from 26 healthy adults at different time points, were quantified by UPLC-MS/MS. Associations between %5mdC and %5hmdC, respectively, and short-term exposure (1-7days) to air pollutants PM2.5 and PM10 were tested with mixed-effects models including various covariates. RESULTS/DISCUSSION Dynamic short-term changes in DNA methylation and hydroxymethylation levels in buccal cells were observed, which were inversely associated with exposure to PM2.5 and PM10. An IQR increase in PM2.5 over a 7-day moving average period was significantly associated with a decrease of -1.47% (-1.74%, -1.20%) and -0.043% (-0.054%, -0.032%) in %5mdC and %5hmdC, respectively. Likewise, for PM10, a decrease of -1.42% (-1.70, -1.13) and -0.040% (-0.051%, -0.028%) was observed. CONCLUSION Global DNA methylation and hydroxymethylatation varied over a time period of three weeks. The observed temporal variability was associated with exposure to ambient PM2.5 and PM10 levels. This should be taken into account when interpreting epigenetic alterations in buccal cells.
Collapse
Affiliation(s)
- Siemon De Nys
- KU Leuven (University of Leuven), Department of Oral Health Sciences, BIOMAT & University Hospitals Leuven (UZ Leuven), Dentistry, Leuven, Belgium
| | - Radu-Corneliu Duca
- Environment and Health, Department of Public Health and Primary Care, KU Leuven (University of Leuven), Kapucijnenvoer 35, 3000 Leuven, Belgium
| | - Tim Nawrot
- Environment and Health, Department of Public Health and Primary Care, KU Leuven (University of Leuven), Kapucijnenvoer 35, 3000 Leuven, Belgium; Centre for Environmental Sciences, Hasselt University, Belgium
| | - Peter Hoet
- Environment and Health, Department of Public Health and Primary Care, KU Leuven (University of Leuven), Kapucijnenvoer 35, 3000 Leuven, Belgium
| | - Bart Van Meerbeek
- KU Leuven (University of Leuven), Department of Oral Health Sciences, BIOMAT & University Hospitals Leuven (UZ Leuven), Dentistry, Leuven, Belgium
| | - Kirsten L Van Landuyt
- KU Leuven (University of Leuven), Department of Oral Health Sciences, BIOMAT & University Hospitals Leuven (UZ Leuven), Dentistry, Leuven, Belgium
| | - Lode Godderis
- Environment and Health, Department of Public Health and Primary Care, KU Leuven (University of Leuven), Kapucijnenvoer 35, 3000 Leuven, Belgium; IDEWE, External Service for Prevention and Protection at Work, Heverlee, Belgium.
| |
Collapse
|
5
|
White SJ, Laros JF, Bakker E, Cambon‐Thomsen A, Eden M, Leonard S, Lochmüller H, Matthijs G, Mattocks C, Patton S, Payne K, Scheffer H, Souche E, Thomassen E, Thompson R, Traeger‐Synodinos J, Vooren S, Janssen B, den Dunnen JT. Critical points for an accurate human genome analysis. Hum Mutat 2017; 38:912-921. [DOI: 10.1002/humu.23238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 04/13/2017] [Accepted: 04/23/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Stefan J. White
- Department of Human Genetics, Leiden University Medical Center The Netherlands
| | - Jeroen F.J. Laros
- Department of Human Genetics, Leiden University Medical Center The Netherlands
- Clinical GeneticsLeiden University Medical Center The Netherlands
- GenomeScan Leiden The Netherlands
| | - Egbert Bakker
- Clinical GeneticsLeiden University Medical Center The Netherlands
| | - Anne Cambon‐Thomsen
- Epidemiology and Public Health Analyses, Inserm and Université Toulouse III Paul Sabatier Toulouse UMR 1027 France
| | - Martin Eden
- Manchester Centre for Health Economics, University of Manchester Manchester UK
| | - Samantha Leonard
- Epidemiology and Public Health Analyses, Inserm and Université Toulouse III Paul Sabatier Toulouse UMR 1027 France
| | - Hanns Lochmüller
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne UK
| | | | | | - Simon Patton
- Central Manchester University Hospitals Foundation Trust, EMQN Manchester UK
| | - Katherine Payne
- Manchester Centre for Health Economics, University of Manchester Manchester UK
| | | | | | - Ellen Thomassen
- Department of Human Genetics, Leiden University Medical Center The Netherlands
| | - Rachel Thompson
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne UK
| | | | | | | | - Johan T. den Dunnen
- Department of Human Genetics, Leiden University Medical Center The Netherlands
- Clinical GeneticsLeiden University Medical Center The Netherlands
| |
Collapse
|